Biology subjects

Saragovi, A.

Publications and source records attributed to Saragovi, A..

6 recordsLinked to original sources

bioRxiv2024

Controlling semiconductor growth with structured de novo protein interfaces

Protein design now enables the precise arrangement of atoms on the nanometer length scales of inorganic crystal nuclei, opening up the possibility of templating the growth of metal oxides including semiconductors. We designed proteins presenting regularly repeating interfaces containing functional groups that organize ions and water molecules, and characterized their ability to bind to and template metal oxides. Two interfaces promoted the growth of hematite under conditions that otherwise resulted in the formation of magnetite. Three interfaces promoted ZnO nucleation under conditions where traditional ZnO-binding peptides and control proteins were ineffective. Designed cyclic assemblies with these ZnO nucleating interfaces lining interior cavities promoted ZnO growth within the cavity. CryoEM analysis of a designed octahedral nanocage revealed atomic density likely corresponding to the growing ZnO directly adjacent to the designed nucleation promoting interfaces. These findings demonstrate that designed proteins can direct the formation of metal oxides not observed in biological systems, opening the door to protein-semiconductor hybrid materials. One Sentence SummaryWe describe the design of structured protein interfaces that bind to, promote, and localize the growth of zinc oxide and hematite, inorganic materials which are not found in biological systems.

bioengineering↗

bioRxiv2024

Limiting mitochondrial-derived ATP transfer to the cytosol enhances T-cell activation

T-cell activation requires a substantial increase in NAD+ production, often exceeding the capacity of oxidative phosphorylation (OXPHOS). To investigate how T cells adapt to this metabolic challenge, we generated T cell-specific ADP/ATP translocase-2 knockout (Ant2-/-) mice. Loss of Ant2, a crucial protein mediating ADP/ATP exchange between mitochondria and cytoplasm, induces OXPHOS restriction by limiting ATP synthase activity, impeding NAD+ regeneration. Interestingly, Ant2-/- naive T cells exhibited enhanced activation, proliferation, and effector functions compared to wild-type controls. Metabolic profiling revealed that these cells adopt an activated-like metabolic program with increased mitobiogenesis and anabolism. Pharmacological inhibition of ANT in wild-type T cells recapitulated the Ant2-/- phenotype, and improved adoptive cell therapy of cancer. Our findings suggest that Ant2-deficient T cells bypass the typical metabolic reprogramming required for activation, leading to enhanced T-cell function. These results highlight the critical role of mitochondrial metabolism in regulating T-cell fate and underscore the therapeutic potential of targeting ANT for immune modulation.

immunology↗

bioRxiv2022

Enhanced methionine cycle suppresses naïve CD8+ T-cell maturation

The metabolic pathways controlling naive CD8+ T (Tn) cell maturation following thymic egress remain mostly undefined. This is important because immature Tn are a major component of peripheral immune tolerance in newborns and under lymphopenia. In this study we demonstrate that TMRM, a mitochondrial membrane potential marker, could be applied to rapidly identify an immature Tn cell population in the periphery. Applying this marker to perform metabolic and proteomic analysis, we show that immature Tn cells maintain accelerated methionine cycle in respect to mature Tn. This unique metabolic state was associated with restricted Tbx21 locus and diminished immune response in vitro and in vivo. Following our findings, we demonstrate that inhibition of methionine cycle leads to rapid functional maturation of Tn and recovery of immune response to stimuli. Our work provides insight into the way the rate of methionine cycling regulates T cell maturation, opening a path for metabolic manipulation of immune tolerance.

immunology↗

bioRxiv2021

Deep learning methods for designing proteins scaffolding functional sites

Current approaches to de novo design of proteins harboring a desired binding or catalytic motif require pre-specification of an overall fold or secondary structure composition, and hence considerable trial and error can be required to identify protein structures capable of scaffolding an arbitrary functional site. Here we describe two complementary approaches to the general functional site design problem that employ the RosettaFold and AlphaFold neural networks which map input sequences to predicted structures. In the first "constrained hallucination" approach, we carry out gradient descent in sequence space to optimize a loss function which simultaneously rewards recapitulation of the desired functional site and the ideality of the surrounding scaffold, supplemented with problem-specific interaction terms, to design candidate immunogens presenting epitopes recognized by neutralizing antibodies, receptor traps for escape-resistant viral inhibition, metalloproteins and enzymes, and target binding proteins with designed interfaces expanding around known binding motifs. In the second "missing information recovery" approach, we start from the desired functional site and jointly fill in the missing sequence and structure information needed to complete the protein in a single forward pass through an updated RoseTTAFold trained to recover sequence from structure in addition to structure from sequence. We show that the two approaches have considerable synergy, and AlphaFold2 structure prediction calculations suggest that the approaches can accurately generate proteins containing a very wide array of functional sites.

biochemistry↗

bioRxiv2020

Cellular water analysis in T cells reveals a switch from metabolic water gain to water influx

Cell growth is driven by the acquisition and synthesis of dry biomass and water mass. This study examines the increase of water in T cells biomass during cell growth. We found that T cell growth is initiated by a phase of slow increase of cellular water, followed by a second phase of rapid increase in water content. To study the origin of the water gain, we developed a novel method, Cold Aqua Trap - Isotope Ratio Mass Spectrometry (CAT-IRMS), which allows analysis of intracellular water isotope composition. Applying CAT-IRMS, we discovered that glycolysis-coupled metabolic water accounts on average for 11 femtoliter (fL) out of the 20 fL of water gained per cell during the slow phase. At the end of the rapid phase, before initiation of cell division, a water influx occurs, increasing the water level by three-fold. Thus, activated T cells switch from acquiring metabolic water to incorporating water from the extracellular medium. Our work provides a method to analyze cell water content and an insight into the way cells regulate their water mass.

biochemistry↗

bioRxiv2020

Systemic hypoxia inhibits T cell response by limiting mitobiogenesis via matrix substrate-level phosphorylation arrest

Systemic oxygen restriction (SOR) is prevalent in numerous clinical conditions including chronic obstructive pulmonary disease (COPD). However, the influence of SOR on T cell protective immunity remains uncharacterized. Here we show the detrimental effect of hypoxia on mitochondrial biogenesis in activated CD8+ T cells. We find that low oxygen diminishes CD8+ T cell viral response in vivo. Using genetic and pharmacological models, we demonstrate that respiratory restriction inhibits ATP dependent matrix processes, all critical for mitochondrial biogenesis. The effect mediated by respiratory restriction could be rescued by TCA cycle re-stimulation, which led to increased mitochondrial matrix localized ATP via substrate-level phosphorylation. Finally, we demonstrate that short exposure to atmospheric oxygen pressure rescues the CD8+ viral response under systemic oxygen restriction in vivo. Our findings reveal the detrimental effect of hypoxia on mitochondrial biogenesis in activated CD8+ T cells and provide a new approach for reducing viral infections in COPD. HighlightsO_LISystemic chronic hypoxia compromises CD8+ T cell activation C_LIO_LIShortly upon activation, T cells cytoplasmic activity becomes independent of mitochondrial ATP outflux C_LIO_LIRespiratory-blockade arrests mitochondrial remodeling due to energy depletion C_LIO_LIUncoupler-based TCA stimulation rescues respiratory-restricted activated CD8+ T cells by stimulating matrix localized substrate-level phosphorylation C_LIO_LICD8+ T cell arrest due to hypoxia in vivo can be rescued by short exposure to atmospheric oxygen pressure. C_LI

immunology↗